6TDT

Thrombin in Complex with a D-DiPhe-Pro-p-pyridine derivative

Summary for 6TDT

• Entry DOI: 10.2210/pdb6tdt/pdb
• Descriptor: Prothrombin, Hirudin variant-2, PHOSPHATE ION, ... (9 entities in total)
• Functional Keywords: coagulation, blood clotting, convertion of fibrinogen to fibrin, blood clotting inhibitor, thrombin inhibitor, preorganization, glycosylation, blood, hydrolase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 36237.10

Authors

Ngo, K.,Heine, A.,Klebe, G. (deposition date: 2019-11-10, release date: 2020-05-13, Last modification date: 2024-01-24)

Primary citation

Ngo, K.,Collins-Kautz, C.,Gerstenecker, S.,Wagner, B.,Heine, A.,Klebe, G.
Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
J.Med.Chem., 63:3274-3289, 2020

PubMed Abstract: Trypsin and thrombin, structurally similar serine proteases, recognize different substrates; thrombin cleaves after Arg, whereas trypsin cleaves after Lys/Arg. Both recognize basic substrate headgroups via Asp189 at the bottom of the S1 pocket. By crystallography and isothermal titration calorimetry (ITC), we studied a series of d-Phe/d-DiPhe-Pro-(amino)pyridines. Identical ligand pairs show the same binding poses. Surprisingly, one ligand binds to trypsin in protonated state and to thrombin in unprotonated state at P1 along with differences in the residual solvation pattern. While trypsin binding is mediated by an ordered water molecule, in thrombin, water is scattered over three hydration sites. Although having highly similar S1 pockets, our results suggest different electrostatic properties of Asp189 possibly contributing to the selectivity determinant. Thrombin binds a specific Na ion next to Asp189, which is absent in trypsin. The electrostatic properties across the S1 pocket are further attenuated by charged Glu192 at the rim of S1 in thrombin, which is replaced by uncharged Gln192 in trypsin.

PubMed: 32011145
DOI: 10.1021/acs.jmedchem.9b02061

Experimental method

X-RAY DIFFRACTION (1.53 Å)